| DT_mohring {lme4breeding} | R Documentation |
Full diallel data for corn hybrids
Description
This dataset contains phenotpic data for 36 winter bean hybrids, coming from a full diallel design and evaluated for 9 traits. The column male and female origin columns are included as well.
Usage
data("DT_mohring")Format
The format is: chr "DT_mohring"
Source
This data was generated by a winter bean study and originally included in the agridat package.
References
Giovanny Covarrubias-Pazaran (2024). lme4breeding: enabling genetic evaluation in the age of genomic data. To be submitted to Bioinformatics.
Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48.
See Also
The core function of the package lmebreed
Examples
data(DT_mohring)
DT <- DT_mohring
head(DT)
DT2 <- add.diallel.vars(DT,par1="Par1", par2="Par2")
head(DT2)
## is.cross denotes a hybrid (1)
## is.self denotes an inbred (1)
## cross.type denotes one way (-1, e.g. AxB) and reciprocal (1, e.g., BxA) and no cross (0)
## cross.id denotes the name of the cross (same name for direct & reciprocal)
## GRIFFING MODEL 2 with reciprocal effects ###########################
## overlay matrix to be added to the addmat argument
Z <- with(DT, overlay(Par1, Par2) )
fema <- (rep(colnames(Z), nrow(Z)))[1:nrow(Z)]
mod1h <- lmebreed(Ftime ~ 1 + (1|Block) +
## GCA male & female overlayed
(1|fema) +
## SCA effects (includes cross and selfs)
(cross.type||cross.id),
addmat=list(fema=Z),
data=DT2 )
vc <- VarCorr(mod1h); print(vc,comp=c("Variance"))
## VarComp VarCompSE Zratio
## Block.Ftime-Ftime 0.00000 9.32181 0.000000
## overlay(Par1, Par2).Ftime-Ftime 1276.73089 750.17269 1.701916
## cross.id.Ftime-Ftime 1110.99090 330.16921 3.364914
## cross.id:cross.type.Ftime-Ftime 66.02295 49.26876 1.340057
## units.Ftime-Ftime 418.47949 74.56442 5.612321
##
## GRIFFING MODEL 2, no reciprocal effects ##############################
mod1h <- lmebreed(Ftime ~ Block + is.cross +
## GCA male & female overlayed main and rr
## GCA effect (calculated only in hybrids; remaining variance)
(is.cross||fema) +
## SCA effect (calculated in hybrids only)
(0+is.cross||cross.id),
addmat=list(fema=Z),
data=DT2 )
vc <- VarCorr(mod1h); print(vc,comp=c("Variance"))
## VarComp VarCompSE Zratio
## overlay(Par1, Par2).Ftime-Ftime 2304.1781 1261.63193 1.826347
## overlay(Par1, Par2):is.cross.Ftime-Ftime 613.6040 402.74347 1.523560
## cross.id:is.cross.Ftime-Ftime 340.7030 148.56225 2.293335
## units.Ftime-Ftime 501.6275 74.36075 6.745864
##
## GRIFFING MODEL 3, no reciprocal effects ###############################
mod1h <- lmebreed(Ftime ~ Block + is.cross +
## GCAC (only for hybrids)
(0+is.cross||fema) +
## male GCA (only for inbreds)
(0+is.self||Par1) +
## SCA (for hybrids only)
(0+is.cross||cross.id),
addmat=list(fema=Z),
data=DT2 )
vc <- VarCorr(mod1h); print(vc,comp=c("Variance"))
## VarComp VarCompSE Zratio
## overlay(Par1, Par2):is.cross.Ftime-Ftime 927.7895 537.91218 1.724797
## Par1:is.self.Ftime-Ftime 9960.9247 5456.58188 1.825488
## cross.id:is.cross.Ftime-Ftime 341.4567 148.53667 2.298804
## units.Ftime-Ftime 498.5974 73.92066 6.745035
##
## GRIFFING MODEL 2, with reciprocal effects #############################
## In Mohring: mixed model 3 reduced
mod1h <- lmebreed(Ftime ~ Block + is.cross +
## GCAC (for hybrids only)
(0+is.cross||fema) +
## male GCA (for selfs only)
(0+is.self||Par1) +
## SCA (for hybrids only)
(0+is.cross||cross.id)+
## SCAR reciprocal effects (remaning SCA variance)
(0+cross.type||cross.id),
addmat=list(fema=Z),
data=DT2 )
vc <- VarCorr(mod1h); print(vc,comp=c("Variance"))
## VarComp VarCompSE Zratio
## overlay(Par1, Par2):is.cross.Ftime-Ftime 927.78742 537.89981 1.724833
## Par1:is.self.Ftime-Ftime 10001.78854 5456.47578 1.833013
## cross.id:is.cross.Ftime-Ftime 361.89712 148.54264 2.436318
## cross.id:cross.type.Ftime-Ftime 66.43695 49.24492 1.349113
## units.Ftime-Ftime 416.82960 74.27202 5.612203
##
## GRIFFING MODEL 3, with RGCA + RSCA ####################################
## In Mohring: mixed model 3
mod1h <- lmebreed(Ftime ~ Block + is.cross +
## GCAC (for hybrids only)
(0+is.cross||fema) +
## RGCA: exclude selfs (to identify reciprocal GCA effects)
(0+cross.type||fema) +
## male GCA (for selfs only)
(0+is.self||Par1) +
## SCA (for hybrids only)
(0+is.cross||cross.id)+
## SCAR reciprocal effects (remaning SCA variance)
(0+cross.type||cross.id),
addmat=list(fema=Z),
data=DT2 )
vc <- VarCorr(mod1h); print(vc,comp=c("Variance"))
## VarComp VarCompSE Zratio
## overlay(Par1, Par2):is.cross.Ftime-Ftime 927.7843 537.88164 1.7248857
## Par1:is.self.Ftime-Ftime 10001.7570 5456.30125 1.8330654
## cross.id:is.cross.Ftime-Ftime 361.8958 148.53670 2.4364068
## overlay(Par1, Par2):cross.type.Ftime-Ftime 17.9799 19.92428 0.9024114
## cross.id:cross.type.Ftime-Ftime 30.9519 46.43908 0.6665054
## units.Ftime-Ftime 416.09922 447.2101 0.93043333
[Package lme4breeding version 1.0.30 Index]